4WSN
Crystal structure of the COP9 signalosome, a P1 crystal form
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4D10 | 4d10 chains A-H |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 273 | CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.73 | 67.01 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 150.638 | α = 92.34 |
b = 150.983 | β = 92.62 |
c = 336.72 | γ = 119.88 |
Symmetry | |
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Space Group | P 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 6M | 2011-06-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X10SA | 1.0004 | SLS | X10SA |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | ||||||
1 | 5.5 | 49.64 | 94.9 | 0.072 | 0.065 | 0.997 | 5.4 | 1.9 | 79098 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 5.5 | 5.61 | 88.7 | 1.329 | 1.205 | 0.166 | 0.6 | 1.9 | 4292 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 4d10 chains A-H | 5.5 | 49.64 | 78769 | 1996 | 96.92 | 0.2548 | 0.2542 | 0.2821 | RANDOM | 125.221 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
7.74 | 3.59 | -3.95 | 7.98 | -5.52 | -22.28 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.218 |
r_dihedral_angle_3_deg | 15.272 |
r_dihedral_angle_4_deg | 13.045 |
r_dihedral_angle_1_deg | 5.567 |
r_angle_refined_deg | 0.839 |
r_angle_other_deg | 0.745 |
r_chiral_restr | 0.047 |
r_bond_refined_d | 0.005 |
r_gen_planes_refined | 0.004 |
r_bond_other_d | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 124422 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 6 |
Software
Software | |
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Software Name | Purpose |
Aimless | data scaling |
XDS | data reduction |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |